From oles@kjemi.uio.no Fri Dec 8 06:56:52 1995 Received: from mons.uio.no for oles@kjemi.uio.no by www.ccl.net (8.6.10/950822.1) id GAA03320; Fri, 8 Dec 1995 06:48:40 -0500 From: Received: from ulrik.uio.no by mons.uio.no with local-SMTP (PP) id <07859-0@mons.uio.no>; Fri, 8 Dec 1995 12:48:14 +0100 Received: by waage.uio.no ; Fri, 8 Dec 1995 12:48:13 +0100 Date: Fri, 8 Dec 1995 12:48:13 +0100 Message-Id: <199512081148.MAA04317@waage.uio.no> To: P8946019@vmsuser.acsu.unsw.EDU.AU CC: chemistry@www.ccl.net In-reply-to: <01HYKDHE6MVG8XQADR@vmsuser.acsu.unsw.EDU.AU> (message from P8946019 on Fri, 08 Dec 1995 13:07:59 +1000) Subject: Re: CCL:Calcs with STOs Hugh, >Do you know if there are any programs that use Slater Type Orbitals, as a basis >set, in circulation? Depends on how you define "circulation". The ADF (Amsterdam Density Functional) package uses STO's as basis functions. Academic customers get it, or at least used to get it, for 1500 dutch guilders (about 1000 USD). Ole Swang From arthur@csb0.IPC.PKU.EDU.CN Fri Dec 8 08:11:52 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id IAA03911; Fri, 8 Dec 1995 08:00:14 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA18204; Fri, 8 Dec 95 20:38:20 -0800 Date: Fri, 8 Dec 1995 20:38:19 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Problem in reading PDB files Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Have you ever used SYBYL? During the last few days, I was astonished to find SYBYL does have problem in reading PDB files. Let me elaborate now. First, I constructed several organic molecules by QUANTA 4.1 then I exported them in PDB files. But when I wanted to perform further QSAR studies on these molecules in SYBYL, I found SYBYL could not read them properly. Oftenly aromatic carbons were ignored and atom connections could not be rebuilt. I checked my PDB files carefully, but I just got no idea. Feeling frustrated, I attempted to use SYBYL to construct a model for test. I saved it in several PDB formats, such as Brookheaven, AMBER Brookhaven and DSCG Brookheaven, which were all listed in the SYBYL menu. When I tried to recall my model from these PDB files, I failed again. It seems that SYBYL does not recognize its own output! You can check it yourself by constructing a molecule as simple as biphenly. When you recall it from the PDB file, I am sure you will find several aromatic carbons are missing. Anyone who has noticed this problem? Or you have good ideas to deal with it? Or you have found my mistake? Arthur in desperation. _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ Arthur Wang Doctoral Candidate _/ _/ _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2501490 Fax: 86-10-2501725 _/ _/ WWW: http://www.ipc.pku.edu.cn/arthur/homepage.html _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-chemistry@ccl.net Fri Dec 8 08:41:52 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA04181; Fri, 8 Dec 1995 08:27:40 -0500 Received: from dira.bris.ac.uk for P.Hindmarch@Bristol.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id IAA25611; Fri, 8 Dec 1995 08:27:33 -0500 (EST) Received: from zeus.bris.ac.uk by dira.bris.ac.uk with SMTP (PP); Fri, 8 Dec 1995 13:26:07 +0000 Received: by zeus.bris.ac.uk (950215.SGI.8.6.10/940406.SGI) id NAA21645; Fri, 8 Dec 1995 13:25:56 GMT From: P.Hindmarch@bristol.ac.uk (Peter Hindmarch) Message-Id: <199512081325.NAA21645@zeus.bris.ac.uk> Subject: Experimental Design Course To: chemed-l@uwf.cc.uwf.edu, chemistry@ccl.net, ics-l@umdd.umd.edu Date: Fri, 8 Dec 1995 13:25:56 +0000 (GMT) Cc: c.l.hutcheon@bristol.ac.uk, cevdet.demir@bristol.ac.uk, D.Cirovic@bristol.ac.uk, K.Kavianpour@bristol.ac.uk, P.hindmarch@bristol.ac.uk, S.P.Gurden@bristol.ac.uk Action: X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Course on Experimental Design School of Chemistry University of Bristol Bristol, UK 25-27 March 1996 Bristol Chemometrics announces a two-and-a-half day course on Experimental Design. Programme --------- The course is aimed at practising scientists who are interested in how experimental design can help in their work, but are not familiar with the wide battery of methods and applications possible. This will not be an advanced course, but be application oriented. The course will cover several topics. Each topic will be organized as a session of approximately one-and-a-half hours in duration, consisting of (a) a lecture, and (b) one or more case studies and / or software demonstration. Software used to demonstrate experimental design will include the spreadsheet Excel and an English language version of the experimental design pacakge NEMROD (authors: R Phan-Tan-Luu and D Mathieu). Three main aspects include screening, optimisation and quantitative modelling. Detailed aspects are as follows. Factorial designs Partial factorial and Plackett-Burman designs ANOVA Simplex and steepest ascent Central composite, face centred cube and star designs D-optimal designs - choice of optimal subset of experiments Mixture designs How confidence in regression models relates to design Design for univariate calibration Design for multivariate calibration Multicriteria optimisation. A wide variety of examples, including analytical chemistry, mixture formulation, synthesis, pharmaceutical chemistry and quality control will be described. Speakers --------- Richard Brereton, Univeristy of Bristol Giuliana Drava, University of Genova. Registration Fee ---------------- The registration fee of #250 includes full documentation of all presentations, all lunches and evening meals, coffee and tea. Accommodation is not included, and accommodation lists can be sent on request. A limited number of concessionary places are available for bona fide students (letter from supervisor required) at a reduced fee of #150. This includes documentation, meals and refreshments but excludes accommodation. Further Details --------------- See WWW page at http://zeus.bris.ac.uk/~chph/brischem.html Email c.l.hutcheon@bris.ac.uk Contact Caroline Hutcheon School of Chemistry University of Bristol Cantock's Close BRISTOL BS8 1TS UK Tel +44 (0)117 928 9000 ext 4421 Fax +44 (0)117 924 1295 From dlarson@thebe.tripos.com Fri Dec 8 12:41:56 1995 Received: from gatekeeper.tripos.com for dlarson@thebe.tripos.com by www.ccl.net (8.6.10/950822.1) id MAA08731; Fri, 8 Dec 1995 12:31:40 -0500 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id LAA08643; Fri, 8 Dec 1995 11:30:29 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma008640; Fri Dec 8 11:30:28 1995 Received: from thebe.tripos (thebe.tripos.com [192.160.145.47]) by tripos.tripos.com (8.6.12/8.6.12) with SMTP id LAA06999; Fri, 8 Dec 1995 11:30:51 -0600 Received: by thebe.tripos (920330.SGI/5.6) id AA18829; Fri, 8 Dec 95 11:30:49 -0600 Date: Fri, 8 Dec 1995 11:30:49 -0600 (CST) From: David Larson Sender: David Larson Reply-To: David Larson Subject: Re: CCL:Problem in reading PDB files To: Arthur Wang Cc: CCL mailing list In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear Dr. Wang I built biphenyl as you described and found that the problem you were having is due to the substructure name PHENYL is truncated to PHE when writing out to a PDB file. When reading the file back in, Sybyl is interpreting the PHE substructure as phenylalanine, rather than phenyl. Modifying the substructure name will solve your problem. Please keep in mind that the PDB file format supports connectivity for amino acids and is not the best file format for saving small organics. As such, importing small organics from PBD format into Sybyl will result in aromatic carbons being modeled as sp2 carbons. Better file formats to use for organics are Sybyl MOL2, MACCS SD, and MACCS MOL. A quick way to change C.2 atoms to C.ar in Sybyl is to modify the atom types using the following SPL: for i in %sln_search2d(m2 C=C=C nodup normal 2) modify atom only $i c.ar endfor Note that you might want to use C=C(Any)=C as the query except that this won't pick up C=C(=Any)=C which may connect phenyls. Please let me know if you have any questions. Best regards, David David Larson e-mail: dlarson@tripos.com Customer Support Scientist phone: 314-647-1099 TRIPOS Inc. fax: 314-647-9241 From netsci@awod.com Fri Dec 8 14:11:58 1995 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.6.10/950822.1) id OAA10340; Fri, 8 Dec 1995 14:04:03 -0500 Received: from [198.81.225.136] (ppp127.awod.com [198.81.225.136]) by sumter.awod.com (8.6.11/8.6.9) with SMTP id OAA00911; Fri, 8 Dec 1995 14:02:56 -0500 X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Dec 1995 15:20:48 +0000 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: December Issue of NetSci Cc: netsci@awod.com The December issue of Network Science (NetSci) is on-line at: http://www.awod.com/netsci/ December highlights the growing problem of Repetitive Strain Injury. This issue also includes the complete listing of 1996 editorial topics as well as a brief summary of a survey highlighting purchasing and use trends in computational chemistry, structure-based drug design and chemical information systems. From smori@utsc.s.u-tokyo.ac.jp Fri Dec 8 21:27:02 1995 Received: from utsc.s.u-tokyo.ac.jp for smori@utsc.s.u-tokyo.ac.jp by www.ccl.net (8.6.10/950822.1) id VAA17336; Fri, 8 Dec 1995 21:13:26 -0500 Received: by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA16555; Sat, 9 Dec 95 11:13:08 JST Date: Sat, 9 Dec 95 11:13:08 JST From: Seiji Mori Message-Id: <9512090213.AA16555@utsc.s.u-tokyo.ac.jp> To: chemistry@www.ccl.net Subject: Summary for NMR isotropy and anitrosopy Dear netters, In the meanwhile, as for the concept of anitrosopy and isotropy, thank you for sending me many replies. I WILL study these concepts and theory. Thank you very much for your help. Sincerely yours, Seiji Mori ---my original questions about isotropy and anisotropy--- Dear Sirs, I posted to CCL about the methods of NMR calculation a fey days ago , and had an other question. In G94, I tried to calculate the chemical shifts , there are magnetic shieldings in the output, however, no chemical shift but isotropic and anitrosopy. I examine meaning of these terms in the user's manual of Gaussian 94 and several original papers,for example, M. Schindler, et al. JCP, 1982, 76, 1919 and Pulay et al. JACS, 1990, 112, 8251, and so on which there is replies of my previous questions , but I only know that isotropic terms is "likely" to be corresponding to the chemical shifts which was experimentally observed. I had had experiments in organic chemistry, and I am now carrying out the ab initio calculations but I amn't much familiar to know the theory of NMR spectroscopy. Would you please tell me the physical meaning of isotropic and anitrosopy, and which is an equivalent of the experimental chemical shift? It is better that you show the references. Sincerely yours, Seiji Mori ---- replies---- ---1--- Date: Tue, 28 Nov 1995 11:10:24 +0100 (MEZ) From: Alexander Christian Backes Konichiwa Mori-san, (S. Mori wrote: In correct in Japanese, Kon-nichiwa.^^:)) the chemical shift is always a tensor (a symmetric 3 x 3 matrix). So, this tensor describes the interchange between several NMR-active nuclei. The outerdiagonal elements are only important in spectra of the solid phase because there the position of the molecules and therefore the observed nuclei are defined and the shift is therefor anisotropic (CSA = Chemnical shift anisotropy). In solution the motion of the molecules is randomized, so the NMR-spectrometer observes the middled shift. This means, the trace of the matrix is relevant (the trace is the sum of the diagonal elemnts of the matrix, divided by three, in case of the 3 x 3 matrix). So, in G94 the calculated isotropic shift is the relevant one for solution. Of course you need a standard for the chemical shift; G94 doesn't know to which reference substance the shifts are related to. So you have to calculate TMS at exactly the same level as the calculated molecule, and then you have to subtract the isotropic data of your molecule from the isotropic data of TMS. (This you have to do each time you use another method and basis set for geometry optimization and NMR-calculations). But be careful - the input geometry of TMS must have Td-symmetry. And therefore you have to precalculate TMS at MP2-level to make sure it gets Td-Symmetry. This geometry you can use as standard input for any of the following calculations of geometry and NMR-parameters. References to the first point you can find in any book dealing with the theory of NMR-spectroscopy. The second point has references first our own experience and second papers which will be published soon. Greetings from Germany, Alexander. ---2--- From: lohrenz@oci.unizh.ch Date: Tue, 28 Nov 1995 13:41:54 +0100 (MET) Hi Seiji, your are probably interested in the isotropic shielding. To convert from shielding to chemical shift (in delta scale) you have to calculate the shielding of a reference compound, say for example TMS for 1H-, 13C- or Si NMR and substract the calculated shielding values of your compound. In principle it is also possible to use smaller references like CH4. In this case you have to take care of the delta-value of this compound (eg. -2.3 ppm for 13C in CH4). Just make sure that you use identical basissets for the calculations. The anisotropic values can sometimes be measured in CPMAS (solid state nmr). They give the shielding along the princible axis of your system. For spherical homogeneous compounds like CH4 you will notice that the anisotropic shieldings are the same as the isotropic. Since solution nmr gives an average of all possible orientations you alway get the isotropic shieldings. Only in cases where the molecule can be oriented (no rotation) like in the solid state, it is possible to measure the three anisotropic values independently. John ---3--- Date: 28 Nov 1995 14:31:34 +0000 From: "E.A.Moore (Elaine Moore)" G94 and all other ab initio programs used for calculating chemical shifts calulate chemical shielding. Experiment measures the chemical shift which is the chemical shielding relative to that of a reference molecule such as TMS (tetramethylsilane). The relative isotropic shielding is the quantity normally observed, for example in liquid samples. The anisotropy can be obtained from solid state measu rements and can be important in relaxation. Chemical shielding is a tensor quantity and G94 gives you all 9 components in the frame you have chosen. The isotropic shielding is (sigma xx + sigma yy + sigma zz)/3. The anisotropy is sigma 33 - (sigma 11 + sigma 22)/2 where 1,2,3 refer to the principal axis frame and sigma 33> sigma 22 >sigma 11. The chemical shift is sigma (reference)- sigma (compound) where sigma is the isotropic shielding. Hope this is some help Elaine A. Moore Chemistry Dept. The Open University UK ---4--- From: evaldera@inti.ivic.ve (Elmer Valderrama) Date: Tue, 28 Nov 1995 09:28:48 +0000 (GMT) Hi, Anisotropy only shows up in ordered media (crystalls, liquid-crystals). Organic compounds may be in solid state. As such, -e.g. not disolved in any solvent-, they may be "measured" in a RMN experiment. If, to this end, a direction of the crystal have been chosen, it may happen that the shift measured in the perpendicular to this chosen direction shows different. Then you'll have a diference which is called anisotropy. Moreover, -and for this it's better to read the reference below-, since the chem. shift actually is a tensor you'd have to compute three components (the diagonal) relative to the chosen direction in the crystal. In isotropic media (a mix of crystalls, no direction can be especified, or in liquid/solved sample) the shift is just the common measured quantity which physically is equal to one third of the trace of the above mencioned tensor. ..my two cents, hope it helps. Elmer Valderrama [1] K. Eichele, et al. "Phosphorus-31 Chemical Shift of Phosphinidene Ligands in Ruthenium Carbonyl Cluster Compounds: A 31-P Single Crystal and CP/MAS-NMR Study" J.Am.Chem.Soc. 1995,117,6961-6969 [and ref there in] (This work includes an orbital study using CACAO and a qualitative application of Ramsey's theory) ---5--- From: willsd@APPSTATE.BITNET To: Mori Seiji Date: Tue, 28 Nov 1995 10:51:13 -0400 (EDT) Seiji: I ran into this proble recently and have a suggestion: 1) You need the isotropic part of the shielding tensor. 2) Chemical shifts can be calculated from this isotropic part using some simple theory: I recommend the information in chapter 2 of : Multinuclear NMR, J. Mason Ed., Plenum Press, New York, 1987. You will also need the isotropic shielding for the chemical shift standard for your nucleus. (In my case it was (EtO)2.BF3 for 11B NMR). Steve Williams Chemistry Appalachian State University Boone, NC 28608 willsd@appstate.edu ---6--- Date: Wed, 29 Nov 1995 12:08:48 +1000 To: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) From: hughc@extro.ucc.su.OZ.AU (Hugh Capper) Dear Mori, isotropic = having the same physical arrangement of moieties around the atom of interest which in this case is the proton ( if you are doing proton specroscopy) anitrosopy = is the reverse ie having different moities which cause diffences around the proton of interest. anitrosopy is reflected in the chemical shift. As for a reference a good basic text is Fundamentals of NMR Spectroscopy by Derome. best wishes, Hugh Capper Institute for Magnetic Resonance Research University of Sydney NSW 2006 Australia ---7--- From: mjf@biosym.com (Mark J Forster ) Date: Tue, 28 Nov 1995 10:03:11 -0800 ( You can see in CCL archive list.) --- end--- #################################################### Seiji Mori Graduate student in Nakamura Laboratory Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@chem.s.u-tokyo.ac.jp #################################################### From smori@utsc.s.u-tokyo.ac.jp Fri Dec 8 21:32:33 1995 Received: from utsc.s.u-tokyo.ac.jp for smori@utsc.s.u-tokyo.ac.jp by www.ccl.net (8.6.10/950822.1) id VAA17324; Fri, 8 Dec 1995 21:12:20 -0500 Received: by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA16544; Sat, 9 Dec 95 11:12:01 JST Date: Sat, 9 Dec 95 11:12:01 JST From: Seiji Mori Message-Id: <9512090212.AA16544@utsc.s.u-tokyo.ac.jp> To: chemistry@www.ccl.net Subject: Summary for NMR chemical shift calculations Dear netters, Thank you for several replies about my questions for the method of NMR chemical shift, and so on. I think the reliability of IGAIM , CSGT in G94 packages were not known very much thus we have to check these methods comparing with known methods. The systematic review of solvent effects, polarity and coordination with donating solvent such as ether have still be awaited. As to couplling constant, I understood the these computational costs since huge of integrals. Recently, I found the application of coupling constant (29Si-7Li) calculation for silyllithiums. At the calculated values at HF/MIDI-4*( truncated ) methods is close to experimental results. ( O, Kikuchi, et al. Organometallics, 1995, 14, 4018 and references cited therein). I show original question and corresponding replies. Thank you very much for your help. Sincerely yours, Seiji Mori ---my original question --- Dear everybody, Recently, many letters about NMR chemical shift calculation were posted, and I am also interested in NMR shifts in organic and organometallic complexes in solution. I have several questions, 1. How is the reliablities of 1.1 methods (GIAO, IGAIM, CSGT, IGLO) 1.2 theory (HF,DFT,MP2...CC) and basis-sets 1.3 How is the solvent effect of polarity on the NMR shift, coupling constant (I think it is not related calcluation , probably it is a fundamental question about NMR)? 2. Do you know the program or references which one can calculate not only chemical shift but also the coupling constant ( for example, 1H-1H and 13C-13C) and NOE in quantum chemistry other than G94? As to 1H-1H coupling constant, many programs such as PCMODEL was supported but its calculation is not QC. If you have comments and indicate the references, would you please send me ? I will summarize replies. Thanks in advance, Seiji Mori ------------- Replies ---1--- Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA10813; Fri, 24 Nov 1995 15:29:30 -0700 From: schrecke@zinc.chem.ucalgary.ca Hi Seiji, you have quite a lot of questions in your posting ... I shall try to give you a few hints, with no intention to be comprehensive. > > 1. How is the reliablities of > 1.1 methods (GIAO, IGAIM, CSGT, IGLO) > 1.2 theory (HF,DFT,MP2...CC) and basis-sets > 1.3 How is the solvent effect of polarity on the NMR shift, coupling > constant > (I think it is not related calcluation , probably it is a fundamental > question about NMR)? Good references to start with are three nice reviews, one new, two are older: D.B.Chesnut: Annual Reports on NMR Spectroscopy, published by Academic Press, Vol.21,1989, p. 51 and ibid, Vol. 29, 1994, p.71. H.Fukui: Magn. Res. Rev. 1987, vol. 11, 205 Further, very comprehensive reviews are contained in an annual series, since 1980 written every year by C.Jameson: in Specialist Periodical Report on Nuclear Magnetic Resonance, Vol.8,1980-... (edited by G.A.Webb, and published by the Royal Society of Chemistry, Cambridge) Now more specific comments on your various questions. 1.1 Methods with distributed gauge origins (IGLO, LORG, GIAO,...) are generally preferable (for a given basis set) over methods with a common gauge origin. For examples, see the various reviews. GIAO seems to converge slightly faster with the size of the basis set then IGLO (see Wolinski, Hinton, Pulay, JACS 1990, 112, 8251). This would also make sense from a theoretical point of view. I don't know off hand about IGAIM, CSGT. 1.2 Correlation. there are cases where correlation is necessary, e.g., M.Buehl et al. J.Phys.Chem. 99, 4000 (1995), and M.Buehl et al. Chem.Phys.Lett. 241 (1995), 248. These papers contain examples where MP2 fails completely to predict the shift while DFT and CCSD are able to achieve quantitative results. There are however many other cases where the HF level works just fine (all the respective literature up to -- say -- five years ago). Basis sets. See about any paper with calculated shifts. E.g., the one by Pulay et al. mentioned above, or various papers by the Kutzelnigg group, or the various reviews. 1.3 Solvation effects can be considerable, indeed. Look for experiments that were done in the gas phase (in addition to solution studies). A review of gas phase NMR was written by C. Jameson: Chem.Rev.1991, 91, 1375. > 2. Do you know the program or references which one can calculate not >only > chemical shift but also > the coupling constant > ( for example, 1H-1H and 13C-13C) and NOE in quantum chemistry >other than > G94? As to 1H-1H > coupling constant, > many programs such as PCMODEL was supported but its calculation is >not QC. Coupling constants are MUCH tougher to calculate than chemical shifts. The reason is (in my opinion) that you are dealing with operators that evaluate the electron density in essentially just one point of space rather than over an entire region of space. Annual reviews of calculations are contained in the same series of books that was metioned before: Specialist Periodical Report on Nuclear Magnetic Resonance Calculations have been done recently, e.g., by Erikson/Malkin/Salahub et al. but I don't have the references on hand right now. I am looking forward to your summary! Yours, Georg ---2--- From: "Steve Gwaltney" Date: Mon, 27 Nov 1995 10:51:20 -0500 > 2. Do you know the program or references which one can calculate not > only > chemical shift but also > the coupling constant > ( for example, 1H-1H and 13C-13C) and NOE in quantum chemistry > other than > G94? As to 1H-1H ACES II can calculate chemical shifts using GIAO's and MBPT(2) wavefunctions. ACES II can also calculate CCSD coupling constants. For information about ACES II contact aces2@qtp.ufl.edu. I believe TURBOMOLE can also calculate chemical shifts, but you should check with them to make sure. Steve ---3--- From: wagenert@Mailer.Uni-Marburg.DE (Wagener Thomas) Subject: CCL:NMR shift and coupling constant calculation Date: Mon, 27 Nov 1995 14:12:47 +0100 (CET) Dear Seiji Mori, since I have finished my thesis on the ab-initio calculation a few month ago, I hopefully can help you with some of your questions. > 1. How is the reliablities of > 1.1 methods (GIAO, IGAIM, CSGT, IGLO) > 1.2 theory (HF,DFT,MP2...CC) and basis-sets > 1.3 How is the solvent effect of polarity on the NMR shift, coupling > constant I had only the opportunity to work with GIAO and IGLO so I can only make a statement on these methods. Basically IGLO and GIAO are quite reliable for the calculation of "standard" organic compounds though the accuracy of the methods is not as high as the experimental accuracy. A rough estimate would be an accuracy of about 5ppm for 13C chemical shifts - probably better. Taking into account that you are comparing gas phase values at absolute zero with values taken from a sample in solution at a temperature of, say, 200-300K that is probably as close as you can get. The computational effort for the IGLO method is somewhat higher than for the GIAO calculation (at HF-level) though the information you get from IGLO is more extensive. Because IGLO works with localized molecular orbitals (LMOs) you get an anlysis of the contribution of the LMOs to the chemical shift while you only get the shielding constant out of the GIAO calculation. IGLO is available at HF level and there is a DFT version using the IGLO code to calculate chemical shifts. The GIAO method in MO theory is available up to CC level though the computational effort is extremely high so the calculation of the shielding constant at such a highly coorelated level is only possible for small molecules. The GAUSSIAN94 manual states that the GIAO module of the program can cope with DFT but I have no experience with that. > 2. Do you know the program or references which one can calculate not > only > chemical shift but also > the coupling constant > ( for example, 1H-1H and 13C-13C) and NOE in quantum chemistry >other than > G94? As to 1H-1H coupling constant, As far as I know (and I really may not be up to date) the only programs capable of calculating coupling constants is DeMon with DFT-IGLO and ACESII (at MP2 level). Some useful references are: - IGLO: Kutzelnigg, W.; Fleischer, U.; Schindler, M.:"The IGLO-Method: Ab- initio Calculation and Interpretation of NMR chemical Shifts and magnetic Susceptibilities", NMR Basic Princ. Prog., Vol. 23, Springer-Verlag, Berlin Heidelberg, 1990, 165 - DFT-IGLO: Malkin, M. G.; Malkina, O. L.; Casida, M. E.; Salahub, D. R., JACS, 116(1994), 5898 - HF-GIAO: Wolinski, K.; Hilton, J. F.; Pulay, P., JACS, 112(1990), 8251 - MP2-GIAO: Gauss, J., Chem. Phys. Lett., 191(1992), 614 Hope, this was of some help Thomas Wagener ---end-- ********************************************************** 　 　　森　聖治 東京大学大学院理学系研究科 物理有機化学講座中村研究室 D1 電話番号：03-3812-2111　内線4369 FAX：　　03-3812-8099 email:smori@chem.s.u-tokyo.ac.jp ********************************************************** From Y0H8797@ACS.TAMU.EDU Fri Dec 8 23:27:04 1995 Received: from VMS2.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.6.10/950822.1) id XAA18646; Fri, 8 Dec 1995 23:23:12 -0500 Date: Fri, 8 Dec 1995 22:23:06 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <951208222306.22265aed@ACS.TAMU.EDU> Subject: Re:crystallographic coordinates->cartesian coordiates >If I have crystallographic coordinates for a molecule (reduced coordinates) >and I want regular cartesian coordinates, can you recommend a conversion >program that handles this? ZORTEP is said to be able to do it. Search on the internet and you'll find the address to download. Yong